Flamio Lab - Research

Research Overview

The Flamio Lab seeks to understand how vertebrate genomes regulate innate immune responses to microbial signals. Our research focuses on the molecular and regulatory mechanisms that control immune activation and tolerance, and how disruptions in these systems contribute to inflammatory disease. We combine experimental studies in human immune cell systems with computational analyses of genomic and transcriptomic datasets to investigate how immune signaling pathways are regulated across multiple levels of gene expression. This expertise also informs conservation studies in native fish species, linking genomic and immune insights to ecological and environmental contexts.

Microbial Sensing and Innate Immune Signaling

Innate immunity begins with the detection of conserved microbial molecules by pattern-recognition receptors. Our work examines how these sensing systems are organized and regulated at the genomic and molecular levels, with particular attention to receptor-mediated pathways such as Toll-like receptor (TLR) signaling. Studies in human immune cell systems allow us to connect mechanisms of microbial sensing to immune-mediated kidney diseases including lupus nephritis (LN) and IgA nephropathy (IgAN).

Post-Transcriptional Control of Innate Immunity

A central focus of the lab is post-transcriptional regulation of immune signaling pathways. We investigate how noncoding RNAs and regulatory features within 3′ untranslated regions (3′UTRs) influence immune gene expression. Processes such as alternative polyadenylation (APA) and other RNA-mediated mechanisms shape transcript stability and translational output, providing important layers of control over innate immune signaling.

Evolutionary Genomics of Immune Regulation

To place immune regulatory mechanisms in a broader biological context, our research integrates comparative genomics across vertebrates. In particular, the lab studies immune gene evolution within Centrarchiformes, a diverse lineage of teleost fishes that provides natural variation in innate immune genes and their regulatory architectures. Comparative analyses reveal conserved regulatory principles as well as lineage-specific innovations in immune signaling, informing conservation of imperiled fishes, such as the mud sunfish (Acantharchus pomotis) and the blackbanded sunfish (Enneacanthus chaetodon).

Integrating Evolution and Human Immunology

By combining mechanistic studies in human immune systems with evolutionary analyses across vertebrates, the lab aims to uncover general principles governing innate immune regulation. These integrative approaches help identify regulatory mechanisms that influence immune function and may contribute to susceptibility to inflammatory disease.